Many horticultural crops have been propagated by vegetative means and the presence of many closely related or duplicated accessions is likely in germplasm collection. Garlic (Allium sativum. L) has been also clonally propagated for thousands of year because it does not produce seed under standard cultivation conditions. Large numbers of molecular markers are needed to discriminate closely related clones or to identify duplicates. One particularly useful to achieve this goal is Amplified Fragment Length Polymorphism (AFLP), which could produce high multiplex informative markers in a single reaction and, therefore could generate sufficient markers to discriminate of duplicated and closely related clones. In recent research for characterization of duplicated and closely related clones AFLP technique were used. Thirty seven garlic clones of different cultivation areas of Iran and three exotic clones were analyzed. Five primer combinations of EcoR I+3 and Mse I+3 showed 330 unambiguous bands which 223 markers (%70/6) were polymorphic. Iranian and three garlic clones were clustered in eight main groups. There were relatively high similarity within (%58-100) and some of clones showed very high similarity (more than %95) even though many of clones have same AFLP banding profile. Eight clones of 1st and eight clones in 5th group (%47 of whole Iranian clones) had no polymorphic bands in their groups and likely can be duplicated clones. In general AFLP technique not only can differentiate species and classify botanical verities but also can discriminate duplicated clones. Finally AFLP technique can decrease costs of conservation plant material by discrimination of duplicate accessions in germplasm collections especially in case of horticulture crops that has been propagated asexually.
